Application of computer-aided tomography techniques to visualize kelp holdfast structure reveals the importance of habitat complexity for supporting marine biodiversity

Ecosystem engineers that increase habitat complexity are keystone species in marine systems, increasing shelter and niche availability, and therefore biodiversity. For example, kelp holdfasts form intricate structures and host the largest number of organisms in kelp ecosystems. However, methods that quantify 3D habitat complexity have only seldom been used in marine habitats, and never in kelp holdfast communities. This study investigated the role of kelp holdfasts (Laminaria hyperborea) in supporting benthic faunal biodiversity. Computer-aided tomography (CT-) scanning was used to quantify the three-dimensional geometrical complexity of holdfasts, including volume, surface area and surface fractal dimension (FD). Additionally, the number of haptera, number of haptera per unit of volume, and age of kelps were estimated. These measurements were compared to faunal biodiversity and community structure, using partial least-squares regression and multivariate ordination. Holdfast volume explained most of the variance observed in biodiversity indices, however all other complexity measures also strongly contributed to the variance observed. Multivariate ordinations further revealed that surface area and haptera per unit of volume accounted for the patterns observed in faunal community structure. Using 3D image analysis, this study makes a strong contribution to elucidate quantitative mechanisms underlying the observed relationship between biodiversity and habitat complexity. Furthermore, the potential of CT-scanning as an ecological tool is demonstrated, and a methodology for its use in future similar studies is established. Such spatially resolved imager analysis could help identify structurally complex areas as biodiversity hotspots, and may support the prioritization of areas for conservation.

Application of computer-aided tomography techniques to visualize kelp holdfast structure reveals the importance of habitat complexity for supporting marine biodiversity

Ecosystem engineers that increase habitat complexity are keystone species in marine systems, increasing shelter and niche availability, and therefore biodiversity. For example, kelp holdfasts form intricate structures and host the largest number of organisms in kelp ecosystems. However, methods that quantify 3D habitat complexity have only seldom been used in marine habitats, and never in kelp holdfast communities. This study investigated the role of kelp holdfasts (Laminaria hyperborea) in supporting benthic faunal biodiversity. Computer-aided tomography (CT-) scanning was used to quantify the three-dimensional geometrical complexity of holdfasts, including volume, surface area and surface fractal dimension (FD). Additionally, the number of haptera, number of haptera per unit of volume, and age of kelps were estimated. These measurements were compared to faunal biodiversity and community structure, using partial least-squares regression and multivariate ordination. Holdfast volume explained most of the variance observed in biodiversity indices, however all other complexity measures also strongly contributed to the variance observed. Multivariate ordinations further revealed that surface area and haptera per unit of volume accounted for the patterns observed in faunal community structure. Using 3D image analysis, this study makes a strong contribution to elucidate quantitative mechanisms underlying the observed relationship between biodiversity and habitat complexity. Furthermore, the potential of CT-scanning as an ecological tool is demonstrated, and a methodology for its use in future similar studies is established. Such spatially resolved imager analysis could help identify structurally complex areas as biodiversity hotspots, and may support the prioritization of areas for conservation.

Analyzing Gene Centres with the Help of the Checklist Method – the Case of Syria

The present survey of species diversity of cultivated plants is the first for Syria. Some cultivated species will be added in the future, because due to the civil war in Syria, it was not possible to visit the country in the frame of the present work, as initially planned. Checklists proved to be a useful tool for overviewing the cultivated plants of selected areas and allow a characterization of the state of plant genetic resources of Syria. Syria has experienced several civilizations. Man settled in this productive land since ancient times and used its resources. However, such use has led to changes in vegetation and decline of wildlife through the country, in seashore areas, interior, mountains, and grassland. Plant domestication and growing started more than 10,000 years ago in West Asia. Since then, plentiful of economic plant species were present and used by man and his domesticated animals. Forming a part of the Fertile Crescent, where many of the world’s agricultural plants have evolved, Syria is extremely rich in agrobiodiversity. Wild progenitors of wheat and barley and wild relatives of many fruit trees such as almonds and pistachio as well as forage species are still found in marginal lands and less disturbed areas. These are threatened by a wide range of human activities, notably modern, extensive agriculture, overgrazing, overcutting and urban expansion. Syria is also considered as part of one of the main centres of origin, according to Vavilov, who had collected in Syria in 1926. The first expeditions to crop fields showed the exclusive nature of cultivated plants in Syria with a high number of endemic forms. Furthermore, Syria is a part of a biodiversity hotspot. Several studies have been performed to study agrobiodiversity in different parts of Syria, but usually on wild species. Many collections have been carried out; however, they focussed preferably on cereals and pulses, and particularly on wheat, like Vavilov’s expedition. Only 30 crops make up the major part of the conserved Syrian crop plant material in the genebank, indicating that most of the remaining 7,000 species of cultivated plants and many other valuable genetic resources species have only been included on a limited scale in the genebank collections. Although a small country (185,180 km2), Syria accommodates numerous ecosystems that allow for a large diversity of plant genetic resources for agriculture ranging from cold-requiring to subtropical crops to live and thrive. Only few references are available in this respect. The aim of the present study was to complete a checklist of Syria’s cultivated plants of agriculture and horticulture excluding plants only grown as ornamental or for forestry. Furthermore, plants taken for reforestation have not been included, if they do not have also agricultural or horticultural uses. Therefore, the inclusion of plants into the checklist follows the same principles as “Mansfeld’s Encyclopedia”. Main sources of information were published literature, floras of Syria, Lebanon and the Mediterranean, as well as Syrian printed sources in Arabic and/or English, reports from FAO on agricultural statistics in Syria, and data from ICARDA and Bioversity International. In addition, personal observations gathered during professional work in the General Commission for Scientific Agricultural Research (GCSAR) in Syria (since 1989) and participation in projects were taken into account. These were: (1) A project on “Conservation and Sustainable Use of Dry Land Agrobiodiversity in the Near East” with participation of Jordan, Lebanon, Syria, and the Palestinian Authority, focussing on landraces and wild relatives of barley, wheat, lentil, alliums, feed legumes, and fruit trees (1999–2005). (2) A project for vegetable landraces (1993–1995) in collaboration with the former International Plant Genetic Resources Institute and the UN Development Programme, in which 380 local vegetable accessions were evaluated. For medicinal plants and fruit trees I was in personal contact with departments of GCSAR and the Ministry of Agriculture and Agrarian Reform, as well as with private organizations. The resulting checklist was compared with the catalogues of crop plants of Italy and a checklist of cultivated plants of Iraq. The cultivated plant species are presented in alphabetical order according to their accepted scientific names. Each entry consists of a nomenclatural part, folk names, details of plant uses, the distribution in Syria (by provinces), a textual description, and references to literature. In total, 262 species belonging to 146 genera and 57 families were identified. Within-species (intraspecific) diversity is a significant measure of the biodiversity. Intraspecific diversity for wild plants has been and remains to be well studied, but for crop plants there are only few results. Mansfeld’s method is an actual logical contribution to such studies. Among the families, the following have the highest number of crop species: Leguminosae (34 spp.), Rosaceae (24), Gramineae (18), Labiatae (18), Compositae (14), Cruciferae (14), Cucurbitaceae (11), Rutaceae (10), Malvaceae (9), Alliaceae (7), and Anacardiaceae (7). The establishment of an effective programme for the maintenance of plant genetic resources in Syria started in the mid-1970s. This programme considered ex situ and in situ collection of the genetic resources of various field crops, fruit trees and vegetables. From a plant genetic resources viewpoint, it is clear that the homegarden is an important location for the cultivation of so-called neglected and underutilized species (neglected from a research side and underutilized from a larger economic side). Such species have so far not received much care from ecologists, botanists and agronomists, and they are considerably under-represented in genebanks.

Movement patterns and habitat use of the silver tip shark ("Carcharhinus albimarginatus") at the Revillagigedo Archipelago

[EN]The Revillegigedo Archipelago Biosphere Reserve is home to several shark species that spend at least part of their life history associated with oceanic islands associated with hotspots of pelagic biodiversity and in particular with apex predators. Silvertip sharks (Carcharhinus albimarginatus) are is commonly found in all the islands of the archipelago. However, very little is known about the spatial and temporal scales of their habitat use and associated ecological role. In this study, we employed passive acoustic telemetry to investigate the residency patterns and migration dynamics of 35 silvertip sharks tagged in three islands of the archipelago (San Benedicto, Socorro and Roca Partida) and monitored for a period of between 7 and 1165 (mean ± SD: 553.7± 354.2) days.

Residential planning, driver mobility and CO2 emission

The literature on residences and citizens’ transports has focused on either reforming traffic managing in response to residential relocation or post-evaluation of urban planning policies or the evolution of the urban spatial form. In a city there are hotspots that attract the citizens and most of the transportation in the city arises as the citizens’ movement between their residence and the hotspots. Little scholarly attention has been devoted to the possibility to minimize citizens’ transportation in the city by the urban planning of residential areas. In this paper we propose a method to evaluate the environmental impact (in terms of CO2-emissions) of urban plans of residential areas. The method is illustrated in a Swedish case of a midsize city which is presently preoccupied with urban planning of new residential areas in response to substantial population growth due to immigration. The residential plans aims to increase the compactness and residential density in the current center and sub centers leads to less CO2 emissions compare to urban expansion to the edge of the city. The plans of concentrated apartment buildings are more effective in meeting residential needs and mitigating CO2 emissions than dispersed single-family houses.

Urban water sustainability: framework and application

Urban areas such as megacities (those with populations greater than 10 million) are hotspots of global water use and thus face intense water management challenges. Urban areas are influenced by local interactions between human and natural systems and interact with distant systems through flows of water, food, energy, people, information, and capital. However, analyses of water sustainability and the management of water flows in urban areas are often fragmented. There is a strong need to apply integrated frameworks to systematically analyze urban water dynamics and factors that influence these dynamics. We apply the framework of telecoupling (socioeconomic and environmental interactions over distances) to analyze urban water issues, using Beijing as a demonstration megacity. Beijing exemplifies the global water sustainability challenge for urban settings. Like many other cities, Beijing has experienced drastic reductions in quantity and quality of both surface water and groundwater over the past several decades; it relies on the import of real and virtual water from sending systems to meet its demand for clean water, and releases polluted water to other systems (spillover systems). The integrative framework we present demonstrates the importance of considering socioeconomic and environmental interactions across telecoupled human and natural systems, which include not only Beijing (the water-receiving system) but also water-sending systems and spillover systems. This framework helps integrate important components of local and distant human–nature interactions and incorporates a wide range of local couplings and telecouplings that affect water dynamics, which in turn generate significant socioeconomic and environmental consequences, including feedback effects. The application of the framework to Beijing reveals many research gaps and management needs. We also provide a foundation to apply the telecoupling framework to better understand and manage water sustainability in other cities around the world.

Revealing Cultural Ecosystem Services through Instagram Images : The Potential of Social Media Volunteered Geographic Information for Urban Green Infrastructure Planning and Governance

With the prevalence of smartphones, new ways of engaging citizens and stakeholders in urban planning and govern-ance are emerging. The technologies in smartphones allow citizens to act as sensors of their environment, producing and sharing rich spatial data useful for new types of collaborative governance set-ups. Data derived from Volunteered Geographic Information (VGI) can support accessible, transparent, democratic, inclusive, and locally-based governance situations of interest to planners, citizens, politicians, and scientists. However, there are still uncertainties about how to actually conduct this in practice. This study explores how social media VGI can be used to document spatial tendencies regarding citizens’ uses and perceptions of urban nature with relevance for urban green space governance. Via the hashtag #sharingcph, created by the City of Copenhagen in 2014, VGI data consisting of geo-referenced images were collected from Instagram, categorised according to their content and analysed according to their spatial distribution patterns. The results show specific spatial distributions of the images and main hotspots. Many possibilities and much potential of using VGI for generating, sharing, visualising and communicating knowledge about citizens’ spatial uses and preferences exist, but as a tool to support scientific and democratic interaction, VGI data is challenged by practical, technical and ethical concerns. More research is needed in order to better understand the usefulness and application of this rich data source to governance.

Life cycle assessment of advanced bioethanol production from pulp and paper sludge

This work evaluates the environmental performance of using pulp and paper sludge as feedstock for the production of second generation ethanol. An ethanol plant for converting 5400 tons of dry sludge/year was modelled and evaluated using a cradle-to-gate life cycle assessment approach. The sludge is a burden for pulp and paper mills that is mainly disposed in landfilling. The studied system allows for the valorisation of the waste, which due to its high polysaccharide content is a valuable feedstock for bioethanol production. Eleven impact categories were analysed and the results showed that enzymatic hydrolysis and neutralisation of the CaCO3 are the environmental hotspots of the system contributing up to 85% to the overall impacts. Two optimisation scenarios were evaluated: (1) using a reduced HCl amount in the neutralisation stage and (2) co-fermentation of xylose and glucose, for maximal ethanol yield. Both scenarios displayed significant environmental impact improvements.

Mobility in vehicular networks with multiple access points to the infrastructure

Nowadays there is a huge evolution in the technological world and in the wireless networks. The electronic devices have more capabilities and resources over the years, which makes the users more and more demanding. The necessity of being connected to the global world leads to the arising of wireless access points in the cities to provide internet access to the people in order to keep the constant interaction with the world. Vehicular networks arise to support safety related applications and to improve the traffic flow in the roads; however, nowadays they are also used to provide entertainment to the users present in the vehicles. The best way to increase the utilization of the vehicular networks is to give to the users what they want: a constant connection to the internet. Despite of all the advances in the vehicular networks, there were several issues to be solved. The presence of dedicated infrastructure to vehicular networks is not wide yet, which leads to the need of using the available Wi-Fi hotspots and the cellular networks as access networks. In order to make all the management of the mobility process and to keep the user’s connection and session active, a mobility protocol is needed. Taking into account the huge number of access points present at the range of a vehicle for example in a city, it will be beneficial to take advantage of all available resources in order to improve all the vehicular network, either to the users and to the operators. The concept of multihoming allows to take advantage of all available resources with multiple simultaneous connections. This dissertation has as objectives the integration of a mobility protocol, the Network-Proxy Mobile IPv6 protocol, with a host-multihoming per packet solution in order to increase the performance of the network by using more resources simultaneously, the support of multi-hop communications, either in IPv6 or IPv4, the capability of providing internet access to the users of the network, and the integration of the developed protocol in the vehicular environment, with the WAVE, Wi-Fi and cellular technologies. The performed tests focused on the multihoming features implemented on this dissertation, and on the IPv4 network access for the normal users. The obtained results show that the multihoming addition to the mobility protocol improves the network performance and provides a better resource management. Also, the results show the correct operation of the developed protocol in a vehicular environment.

Harvesting and Collection of Animal Forest Species

The harvest and trade of corals and other benthic organisms from the world’s shallow tropical reefs is a lucrative industry that can have positive socioeconomic benefits for communities while supplying the increasing demand specimens for aquaria and curios. For most countries, this trade has historically been almost entirely unregulated. More recently, in response to concerns about the rapid decline of some reefs in the face of anthropogenic and natural pressures, as well as indications of depletions and even localized extinctions of some species caused by harvesting, there have been attempts to improve the sustainability of the industry. Both developing and developed countries face different impediments to this reform, the most pressing and common of which is the lack of reliable data on world trade through CITES. Thereafter, differences in the processes through which reform can be implemented are based principally on the length of the supply chain from collection to export, the degree of industry stewardship, and resourcing. The coral collection fishery in Queensland, Australia, provides an example where continual improvements in reporting and risk assessments and adopting a comanagement approach are delivering better adaptive management of the resource, although the on-ground sustainability benefits of this approach are still to be tested. A simpler approach to sustainable use of coral is to favor the replacement of wild harvested specimens with those bred or grown entirely in an aquaculture facility (as opposed to merely collected and then grown out in culture). Yet there are major impediments to this change, including the dependence of many public aquaria on the same sources as the hobbyist community, difficulties of culturing some species in captivity, and infrastructure costs. Nevertheless, this approach will likely play an important part in reef conservation efforts in the future.

Caractérisation et délimitation des sous-espèces de Gesneria viridiflora (Gesneriaceae) dans les Antilles

Une taxonomie révisée et une connaissance des limites d’espèces demeurent toujours importantes dans les points chauds en biodiversité comme les Antilles où de nombreuses espèces endémiques sont retrouvées. Des limites d’espèces divergentes impliquent un différent nombre d’espèces retrouvées dans un écosystème, ce qui peut exercer une influence sur les décisions prises face aux enjeux de conservation. Les genres Gesneria et Rhytidophyllum qui forment les principaux représentants de la famille des Gesneriaceae dans les Antilles comprennent plusieurs taxons aux limites d’espèces ambigües et quelques espèces qui ont des sous-espèces reconnues. C’est le cas de Gesneria viridiflora (Decne.) Kuntze qui comprend quatre sous-espèces géographiquement isolées et qui présentent des caractères végétatifs et reproducteurs similaires et variables. Une délimitation d’espèces approfondie de ce complexe d’espèce est effectuée ici à partir d’une approche de taxonomie intégrative considérant des données morphologiques, génétiques et bioclimatiques. Les données morphologiques quantitatives et qualitatives obtenues à partir de spécimens d’herbier sont utilisées pour délimiter des groupes morphologiques à l’aide d’une analyse en coordonnées principales. Ces groupes sont ensuite testés à l’aide de séquences d’ADN de quatre régions nucléaires en utilisant une méthode bayesienne basée sur la théorie de la coalescence. Finalement, les occurrences et les valeurs de variables de température et de précipitation qui y prévalent sont utilisées dans une analyse en composantes principales bioclimatique pour comparer les groupes délimités morphologiquement et génétiquement. Les résultats de l’analyse morphologique multivariée supportent la distinction entre les groupes formés par les sous-espèces actuellement reconnues de G. viridiflora. Les résultats, incluant des données génétiques, suggèrent une distinction jusqu’ici insoupçonnée des populations du Massif de la Hotte au sud-ouest d’Haïti qui sont génétiquement plus rapprochées des populations de Cuba que de celles d’Hispaniola. Bioclimatiquement, les groupes délimités par les analyses morphologiques et génétiques sont distincts. L’approche de taxonomie intégrative a permis de distinguer cinq espèces distinctes plutôt que les quatre sous-espèces acceptées jusqu’à aujourd’hui. Ces espèces sont : G. acrochordonanthe, G. quisqueyana, G. sintenisii, G. sylvicola et G. viridiflora. Une carte de distribution géographique, un tableau de la nouvelle taxonomie applicable et une clé d’identification des espèces sont présentés. La nouvelle taxonomie déterminée dans cette étude démontre un endémisme insoupçonné dans plusieurs régions du point chaud en biodiversité des Antilles et souligne l’importance d’investiguer les limites d’espèces dans les groupes diversifiés comprenant des taxons aux limites d’espèces incomprises.

Infra-estrutura do projecto: SEMCABO-WIFI

Esta tese consiste no estudo, implementação e desenvolvimento da infra-estrutura para o projecto SEMCABO-WIFI. Este projecto está inserido na empresa Sem¬ Cabo, com o objectivo de levar a Internet aos clientes sob a forma de hotspots ou no acesso à ultima milha (Last Míle Access) à casa dos residentes. O projecto também deu origem à própria empresa, levando esta a ISP desde Setembro de 2007. Numa primeira fase, é feita abordagem a Sistemas de Authentícatíon, Authorization e Ac­countíng para ISPs, na vertente WI-FI e apresentadas possíveis soluções comercias e open source. Em seguida, é apresentado a empresa SemCabo, vertente comercial e tecnológica. O sistema base da SemCabo é referido, contemplando a tecnologia de suporte, rede, equipamentos activos, módulos de emissão de sinal WI-FI, segurança, monitorização e portal de autenticação. Os servidores base são indicados posteriormente, sendo efectuado a apresentação de todos os servidores com suporte ao projecto, incluindo alguns pormenores de configuração. São apresentados equipa­ mentos e sistemas utilizados para controlo de acesso à rede (NAS), sendo igualmente descritos pormenores de configuração. ABSTRACT; This thesis is about the study, implementation and development of the infrastructure created for the SEMCABO-WIFI project. This project is inserted in the company SemCabo, with the objective to bring the Internet to costumers in the form of hots­pots or access in last mile to the house of residents. The project also originated the company and led the company to ISP since September 2007. ln the first fase, the approach is about Systems Authentication, Authorization and Accounting for WISPs and presented possible commercial and open source solutions. ln next, the SemCabo company is presented and described their technological and commercial aspects. The base system of the SemCabo is refered, considering the support technology, network equipment, modules emission signal WI-FI, security, monitoring and portal authentication module. Base servers of the SemCabo project are shown, a presentation of all the servers that support the project is made, including some details of the configuration. The equipment and systems used to control network access (NAS) are presented, details of configuration are also described.

Improving drug discovery using hybrid softcomputing methods

Virtual screening (VS) methods can considerably aid clinical research, predicting how ligands interact with drug targets. Most VS methods suppose a unique binding site for the target, but it has been demonstrated that diverse ligands interact with unrelated parts of the target and many VS methods do not take into account this relevant fact. This problem is circumvented by a novel VS methodology named BINDSURF that scans the whole protein surface in order to find new hotspots, where ligands might potentially interact with, and which is implemented in last generation massively parallel GPU hardware, allowing fast processing of large ligand databases. BINDSURF can thus be used in drug discovery, drug design, drug repurposing and therefore helps considerably in clinical research. However, the accuracy of most VS methods and concretely BINDSURF is constrained by limitations in the scoring function that describes biomolecular interactions, and even nowadays these uncertainties are not completely understood. In order to improve accuracy of the scoring functions used in BINDSURF we propose a hybrid novel approach where neural networks (NNET) and support vector machines (SVM) methods are trained with databases of known active (drugs) and inactive compounds, being this information exploited afterwards to improve BINDSURF VS predictions.

Improving drug discovery using a neural networks based parallel scoring function

Virtual Screening (VS) methods can considerably aid clinical research, predicting how ligands interact with drug targets. Most VS methods suppose a unique binding site for the target, but it has been demonstrated that diverse ligands interact with unrelated parts of the target and many VS methods do not take into account this relevant fact. This problem is circumvented by a novel VS methodology named BINDSURF that scans the whole protein surface to find new hotspots, where ligands might potentially interact with, and which is implemented in massively parallel Graphics Processing Units, allowing fast processing of large ligand databases. BINDSURF can thus be used in drug discovery, drug design, drug repurposing and therefore helps considerably in clinical research. However, the accuracy of most VS methods is constrained by limitations in the scoring function that describes biomolecular interactions, and even nowadays these uncertainties are not completely understood. In order to solve this problem, we propose a novel approach where neural networks are trained with databases of known active (drugs) and inactive compounds, and later used to improve VS predictions.

Multilocus genetic analyses provide insight into speciation and hybridization in aquatic grasses, genus Ruppia

Aquatic plants of the genus Ruppia inhabit some of the most threatened habitats in the world, such as coastal lagoons and inland saline to brackish waters where their meadows play several key roles. The evolutionary history of this genus has been affected by the processes of hybridization, polyploidization, and vicariance, which have resulted in uncertainty regarding the number of species. In the present study, we apply microsatellite markers for the identification, genetic characterization, and detection of hybridization events among populations of putative Ruppia species found in the southern Iberian Peninsula, with the exception of a clearly distinct species, the diploid Ruppia maritima. Microsatellite markers group the populations into genetically distinct entities that are not coincident with geographical location and contain unique diagnostic alleles. These results support the interpretation of these entities as distinct species: designated here as (1) Ruppia drepanensis, (2) Ruppia cf. maritima, and (3) Ruppia cirrhosa. A fourth distinct genetic entity was identified as a putative hybrid between R. cf. maritima and R. cirrhosa because it contained a mixture of microsatellite alleles that are otherwise unique to these putative species. Hence, our analyses were able to discriminate among different genetic entities of Ruppia and, by adding multilocus nuclear markers, we confirm hybridization as an important process of speciation within the genus. In addition, careful taxonomic curation of the samples enabled us to determine the genotypic and genetic diversity and differentiation among populations of each putative Ruppia species. This will be important for identifying diversity hotspots and evaluating patterns of population genetic connectivity. © 2015 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, 00, 000–000.